The objective of this work is to correlate the accumulation of trace elements in food tubers with possible alterations of the secondary plant metabolism. Samples of carrots, onions and potatoes grown in the environmentally polluted area of Asopos river in Viotia, Greece and other Greek areas (control) were analysed for carotenoids by HPLC-UV and DPPH antioxidant activity. In carrots, the levels of α-carotene, β-carotene and lutein were quantified and it was found that Asopos samples had statistically significantly lower levels of β-carotene compared to control ones. Also, in potatoes, the levels of lutein in Asopos samples were statistically significantly lower than control ones. However, in onions, the levels of lutein between Asopos and control samples were not found statistically different. In all samples, no statistically significant differences in the levels of DPPH activity (measured as ΙC50: sample levels that cause 50% inhibition of DPPH scavenging activity) were observed. In conclusion, the presence of heavy metals in carrots and potatoes has affected the levels of carotenoids.